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From language models to large-scale food and biomedical knowledge graphs
Gjorgjina Cenikj, Lidija Strojnik, Risto Angelski, Nives Ogrinc, Barbara Koroušić-Seljak, Tome Eftimov, 2023, original scientific article

Abstract: Knowledge about the interactions between dietary and biomedical factors is scattered throughout uncountable research articles in an unstructured form (e.g., text, images, etc.) and requires automatic structuring so that it can be provided to medical professionals in a suitable format. Various biomedical knowledge graphs exist, however, they require further extension with relations between food and biomedical entities. In this study, we evaluate the performance of three state-of-the-art relation-mining pipelines (FooDis, FoodChem and ChemDis) which extract relations between food, chemical and disease entities from textual data. We perform two case studies, where relations were automatically extracted by the pipelines and validated by domain experts. The results show that the pipelines can extract relations with an average precision around 70%, making new discoveries available to domain experts with reduced human effort, since the domain experts should only evaluate the results, instead of finding, and reading all new scientific papers.
Keywords: biomedical knowledge graphs, relation-mining pipelines, relation extraction, validation
Published in DiRROS: 17.05.2023; Views: 208; Downloads: 90
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Post-fire effects on development of leaves and secondary vascular tissues in Quercus pubescens
Jožica Gričar, Polona Hafner, Martina Lavrič, Mitja Ferlan, Nives Ogrinc, Bor Krajnc, Klemen Eler, Dominik Vodnik, 2020, original scientific article

Abstract: An increased frequency of fire events on the Slovenian Karst is in line with future climate-change scenarios for drought-prone environments worldwide. It is therefore of the utmost importance to better understand tree-fire-climate interactions for predicting the impact of changing environment on tree functioning. To this purpose, we studied the post-fire effects on leaf development, leaf carbon isotope composition (%13C), radial growth patterns and the xylem and phloem anatomy in undamaged (H-trees) and fire-damaged trees (F-trees) of Q. pubescens with good re-sprouting ability in spring 2017, the growing season after a rangeland fire in August 2016. We found that the fully developed canopy of F-trees reached only half of the LAI values measured in H-trees. Throughout the season, F-trees were characterised by higher water potential and stomatal conductivity and achieved higher photosynthetic rates compared to unburnt H-trees. The foliage of F-trees had more negative %13C values than those of H-trees. This reflects that F-trees less frequently meet stomatal limitations due to reduced transpirational area and more favourable leaf-to-root ratio. In addition, the growth of leaves in F-trees relied more on the recent photosynthates than on reserves due to the fire disturbed starch accumulation in the previous season. Cambial production stopped 3 weeks later in F-trees, resulting in 60% and 22% wider xylem and phloem increments, respectively. A novel approach by including phloem anatomy in the analyses revealed that fire caused changes in conduit dimensions in the early phloem but not in the earlywood. However, premature formation of the tyloses in the earlywood vessels of the youngest two xylem increments in F-trees implies that xylem hydraulic integrity was also affected by heat. Analyses of secondary tissues showed that although xylem and phloem tissues are interlinked changes in their transport systems due to heat damage are not necessarily coordinated.
Keywords: pubescent oak, cambium, radial growth, xylem, phloem, anatomy, sub-Mediterranean
Published in DiRROS: 19.03.2020; Views: 2216; Downloads: 1192
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